(CNN) -- Federal investigators are concerned a potential danger persists because of the simultaneous use of intersecting runways at Newark Liberty International Airport, one of the nation's busiest and a gateway to the New York metro area.

The alert comes after repeated instances in which planes above the Newark airport flew too close to each other in violation of safety standards. There were four such instances last year and at least four this year, according to the U.S. Department of Transportation inspector general.

In one case, on January 16, 2008, two Continental planes -- a Boeing B-737 and an Embraer 145 -- missed each other by 600 feet, according to a DOT inspector general's report.

"That was very scary. I was there for that one personally in the control tower, and it scared the heck out of everybody up there," said Ray Adams, a Newark air traffic controller.

Potential danger arises when approaching planes need to abort their landings, which happens about every 700 flights at Newark, according to a Federal Aviation Administration analysis.

In what the FAA calls "go-arounds," the diverted plane approaching Newark has to make a sharp right turn through the flight path of planes landing and taking off from an intersecting runway, allowing little margin for error.

"There was a distinct possibility that we could have had a collision with these operations," Adams said.

Adams said he raised the safety issue to the FAA but got nowhere. He persisted, taking his complaint to New Jersey's congressional delegation, which organized two meetings last year with FAA officials.

In response, Adams said, he was punished, put on paid leave for 11 months, then leave without pay for a month. The FAA said the disciplinary actions had nothing to do with Adams' safety complaints.

Adams filed a whistle-blower complaint with the U.S. Office of Special Counsel, the agency that investigates whistle-blower complaints. Adams' complaint led DOT Inspector General Calvin Scovel to investigate. Scovel found merit in Adams' concerns, concluding in a report two months ago that "questions about the safety of the runway 22L-11 approach configuration at Newark persist."

In response, the FAA promised to use a computer program that helps air traffic controllers stagger aircraft to ensure proper spacing.

On November 5, the DOT wrote to the Office of Special Counsel confirming the computer system had been put to use at Newark on October 26. The next day the Office of Special Counsel learned the technology was no longer in use at Newark.

"I am outraged," said Rep. Donald Payne, D-New Jersey. "When you put into jeopardy the human lives at risk, it can't get any more serious than that."

FAA spokesperson Laura Brown said, "There was no intent to deceive anyone about what we were doing." She added, "FAA safety officers wanted to make absolutely sure employees were fully trained on the equipment." The FAA said it intends to have the computer system fully operational at Newark by mid-December.

Last week the Office of Special Counsel raised the matter with President Obama, writing that "we found a substantial likelihood that FAA officials were engaging in conduct that constitutes gross mismanagement and a substantial and specific danger to public safety."

Meanwhile, after a year out of the control tower, Adams returned to his regular job Wednesday at Newark air traffic control.